I am working with some colleagues at WordCamp Kathmandu contributor day and we are discussing your issue.

Problem 1
While inspecting your site on search listing page we found that the Image of Flower Amethist post is bigger than others which is why the text is shifted to the right and the post after Flower Amethist is also not correctly display because no clearing has been used and it went to the area where it can fit itself.

So I recommend you to use same image size that you have used in other posts which will solve this design issue.

Problem 2
Your search listing page is listing the post on the portfolio page. IT may be due to some plugins try to deactivate your plugins one by one and find out the plugin that has been adding numbers to your search page.

Thank you.

Best Regards!!